BioC 3.3: CHECK report for GeneBreak on linux2.bioconductor.org

Package: GeneBreak

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.1.0.tar.gz

StartedAt: 2015-10-27 04:05:01 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:08:00 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 179.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GeneBreak.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneBreak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneBreak’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GeneBreak’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [76s/76s] OK
Examples with CPU or elapsed time > 5s
                                                 user system elapsed
bpPlot-CopyNumberBreakPoints-method             9.647  0.036   9.683
bpStats-CopyNumberBreakPoints-method            9.478  0.012   9.494
CopyNumberBreakPointGenes-class                 7.683  0.076   7.761
recurrentGenes-CopyNumberBreakPointGenes-method 7.415  0.012   7.427
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘GeneBreak’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘segmentData’ in package ‘GeneBreak’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneBreak)

name	user	system	elapsed
CopyNumberBreakPointGenes-class	7.683	0.076	7.761
CopyNumberBreakPoints-class	1.593	0.024	1.621
accessOptions-CopyNumberBreakPoints-method	0.857	0.020	0.877
addGeneAnnotation-CopyNumberBreakPoints-method	2.587	0.012	2.606
bpFilter-CopyNumberBreakPoints-method	2.003	0.016	2.027
bpGenes-CopyNumberBreakPointGenes-method	3.866	0.004	3.871
bpPlot-CopyNumberBreakPoints-method	9.647	0.036	9.683
bpStats-CopyNumberBreakPoints-method	9.478	0.012	9.494
breakpointData-CopyNumberBreakPoints-method	1.520	0.196	1.716
breakpointsPerGene-CopyNumberBreakPointGenes-method	3.800	0.204	4.009
callData-CopyNumberBreakPoints-method	1.354	0.184	1.538
featureChromosomes-CopyNumberBreakPoints-method	1.182	0.008	1.190
featureInfo-CopyNumberBreakPoints-method	3.035	0.044	3.079
featuresPerGene-CopyNumberBreakPointGenes-method	3.310	0.028	3.338
geneChromosomes-CopyNumberBreakPointGenes-method	3.727	0.040	3.767
geneInfo-CopyNumberBreakPointGenes-method	3.207	0.036	3.244
getBreakpoints	1.467	0.016	1.483
namesFeatures-CopyNumberBreakPoints-method	0.807	0.012	0.819
recurrentGenes-CopyNumberBreakPointGenes-method	7.415	0.012	7.427
sampleNames-CopyNumberBreakPoints-method	0.830	0.008	0.838
segmentData-CopyNumberBreakPoints-method	1.376	0.140	1.516